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exam 2 Flashcards

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1
Q

DNA Strand

A
  • written 5’ to 3’
  • has bases: guanine, adenine, thymine, cytosine
  • polar ends
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2
Q

which bond pairs bases?

A

hydrogen bonds
noncovalent
attracted through electronegativity

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3
Q

base pairs

A

A + T = adenine + thymine
- only 2 hydrogen bonds
G + C = guanine + cytosine
- 3 hydrogen bonds, strongest

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4
Q

purines

A

A and G (pure as gold)
- have two rings
- pair with pyrimidines

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5
Q

why can’t G bond with T?

A

oxygens can not bind

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6
Q

if the human genome is 30% adenine, how much percentage is it cytosine?

A

20%
- 30 and 30 of A and T
40 of C + G, so 40/2 = 20

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7
Q

DNA is double stranded

A
  • has 2 polynucleotide chains that are held together by hydrogen bonds
  • bases are inward
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8
Q

what kind of backbone does DNA have?

A

sugar-phosphate
- energetically favored

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9
Q

is the backbone hydrophilic or hydrophobic?

A

hydropillic! bases are hydrophobic

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10
Q

what happens if you pair a purine with a purine? pyrimidine with pyrimidine?

A

width is altered

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11
Q

DNA strand parallel?

A

yes! needs to be antiparallel for pairing to occur

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12
Q

what form is DNA?

A

helix
- takes ten pairs for a complete turn
- energetically favorable

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13
Q

what forces support the structure?

A

van der waals

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14
Q

where is information found in DNA?

A

encoded in order of nucleotides
- A, C, T, G
- biological alphabet

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15
Q

what is different in sequences?

A

different messages
- look the same but say different things

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16
Q

DNA packaging

A

3 billion base pairs in 2 meters of DNA

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17
Q

how are the 2 meters of DNA packed?

A

chromosomes

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18
Q

how many pairs of chromosomes?

A

23 in somatic cells
- not reproductive
- each pair is inherited

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19
Q

what is genome?

A

genetic info in chromosomes

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20
Q

what is DNA wrapped around with?

A

histone - protein
- reduces length by 1/3rd

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21
Q

what is a histone complex called?

A

nucleosome - 8 histone wrapped molecules, 147 pairs

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22
Q

what is the charge of histones?

A

positively charge proportion of amino acids - 4 histones

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23
Q

what is chromatin?

A

nucleosomes packed on top of one another

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24
Q

shape of chromatin?

A

folded loops

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25
Q

what do chromatin loops turn into?

A

chromosomes - stops packaging

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26
Q

why is there a lot of lysine and arginine in histones?

A

they enable histones to bind to sugar phosphate backbone

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27
Q

why do chromatins change in structure?

A

to allow gene response

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28
Q

what is used to loosen up DNA?

A

ATP energy - push to histone octamer

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29
Q

what happens to DNA with the complex?

A

DNA is less accessible

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30
Q

what are histone tails?

A
  • play an important role in chromatin structure
  • end that sticks out in N-Terminal
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31
Q

how are tails modified?

A

chemical groups

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32
Q

why is DNA replication necessary?

A

need to replace dead cells - lose about 10 to the eleventh cells per year (about mass of body weight)

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33
Q

what is DNA replication used for?

A

growing - embryonic development - growing in children and adolescents - immune response w/ proliferation of B-cell w/ antibody

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34
Q

what does it mean for DNA to be semiconservative?

A

each parent strand is the template for the mew strand which is a complement

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35
Q

DNA mechanism

A
  1. unwind helix to make template strands
  2. new nucleotides form base pairs with template - link 5’ to 3’
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36
Q

what way should DNA always go?

A

ALWAYS 5’ TO 3’

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37
Q

origin of replication

A
  • begins replication
  • initiator proteins recognize unique DNA sequences
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38
Q

which bases are highly seen in ORI?

A

A and T - easier to remove due to less hydrogen bonding

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39
Q

how many ORIs are there?

A

MANY

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40
Q

what direction is ORI?

A

bidirectional - proceed from replication fork
bubbles get larger and larger

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41
Q

ORI in e-coli?

A

DNA is unwound and proceeds in both directions

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42
Q

what does helicase do?

A

separates 2 strands of DNA + is the 1st replication enzyme
- unwinds DNA + breaks hydrogen bonds

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43
Q

single strand branding proteins

A

prevent H-Bonds from reforming

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44
Q

what is torsional stress?

A

super coiling -> rope is twisting on itself

45
Q

topoisomere

A

create breaks (phosphodiester bonds) to relieve torsional stress

46
Q

what does replication begin with?

A

primer -> shorter RNA sequence
primer = complimentary to DNA template (ribose sugar, uracil instead of thymine)

47
Q

primase

A

synthesizes short sequence

48
Q

why cant DNA polymerase synthesize DNA?

A

needs primer + bind

49
Q

what does the sliding clamp do?

A

maintains DNA polymerases association with template

50
Q

which way is DNA read? grow?

A

read 5’ to 3’, grows 3’ to 5’

51
Q

what does polymerase do?

A

catalyzes condensation reactions
- add nucleotides through formation of phosphodiester bonds

52
Q

how does DNA polymerase extend?

A

from primer until previous primer - gaps w/ no phosphodiester linkages

53
Q

leading strand

A

go forward

54
Q

lagging

A

go back w/ okazaki

55
Q

are lagging and leading related?

A

yes, coupled -> replication of strand w/ discontinuous synthesis

56
Q

what does nuclease do?

A

remove RNA primer

57
Q

final polymerase step

A

fills gaps - complementary DNA

57
Q

what does ligase at end do?

A

seals gap by forming phosphodiester linkages through discontinuous strands

58
Q

how many base pairs are lost w/ cell division?

A

70-100
- lagging strand is incompletely replicated

59
Q

telomerase

A
  • reverse transcription - DNA from RNA
60
Q

when is telomerase active?

A

development + stem cells

61
Q

what happens to repeats?

A

slowly eaten away

62
Q

telomerase as buffer

A

protects internal chromosome region
- combines w/ end that can’t replicate

63
Q

telomere

A

repetitive sequence @ ends of linear chromosomes that act as buffer

64
Q

small genetic change

A
  • base pair chnages - gain genes
  • helps with evolutions
65
Q

harmful mutations

A

can cause diseases - cancer, inheritable genetic diseases (sickle cell, huntingtons), cystic fibrosis (multiple mutations)

65
Q

silent mutations

A

have no effect - in non coding + no chnage in proteins

66
Q

what happens to damage during DNA replication?

A

proofreading ability of DNA polymerases corrects it

67
Q

how many sites does DNA polymerase proofreading have

A

have 2 active sites - editing + polymerizing

68
Q

how do incorrect nucleotides fall off?

A

polymerase bonds loosely and has to change conformation to catalyze phosphodiester bonds

69
Q

what happens when an incorrect nucleotide is added?

A

newly synthesized DNA unpairs
3’ moves into editing -> cannot edit with 3’ to 5’

70
Q

where does most of damage come from?

A

reactive chemicals - produced in cell metabolism
environmental -> uv light, radiation, toxic chemicals

71
Q

what do protein machines do?

A

scan DNA damage - most is temporary

72
Q

how does a double helix help in repair?

A

has 2 copies of genetic info
when one is damaged, the other serves as a source

73
Q

what does damage create?

A

structures not seen in DNA
if it is not fixed b4 replication, there is permanent damage

74
Q

1st step of DNA repair mechanism

A

damage is recognized + excised by nucleases

75
Q

2nd step of DNA repair mechanism

A

repair DNA polymerase binds to 3’ hydroxyl
- fills in the missing nucleotide using undamaged DNA template

76
Q

3rd step of DNA repair mechanism

A

ligase seals nick in helix

77
Q

what is mismatch repair?

A

bases that are not complementary

78
Q

how do you predict the cell determines it needs to make a correction?

A

look for nicks

79
Q

depurination

A

guanine + adenine are removed spontaneuously

80
Q

deamination

A

cytosine is deaminated - removed and produces uracil
adenine is deaminated - produces hypoxanthine and pairs with cytosine

81
Q

if C is deaminated, what would be the sequence of GCAT after a second replication?

A

GTAT - first = CUTA then GTAT

82
Q

what happens after UV damage?

A
  • pyrimidine dimers
  • thymine absorbs UV and becomes reactive w/ adjacent thymine
83
Q

what is the effect of dimers?

A

polymerase cannot read through dimers
- causes distortion in backbone that is recognized by repair proteins

84
Q

repaired dimers

A

90% of dimers are repaired in minutes

85
Q

nonhomologous end joining

A

cells try to repair before 2 fragments drift
- error prone process bc nucleotides can be lost

86
Q

homologous recombination

A

homologous DNA is the template for DNA
ONLY if break is right after replication
- error free process

87
Q

what causes nonhomologous breaks?

A

caused by replication fork (chemical assaults)
- no mechanism to replace info
- cells try to quickly repair before 2 fragments drift

88
Q

what does nuclease do in nonhomologous end joining?

A

clean up ends

89
Q

what does ligase do in nhej?

A

joins ends

90
Q

what is homologous recombination?

A

only happens after replication
- one of the broken 3’ ends invades homologous DNA duplex -> looking for complementary sequence

91
Q

what happens to the invading strand in HR?

A

invading strand = elongated by repair polymerase

92
Q

what is PCR used for?

A

amplify small DNA segments - molecular photocopying
- need significant amounts of DNA
can also detect virus, study genome, diagnosis

93
Q

what is needed to replicate DNA?

A

template sequence
way to separate double stranded DNA (heat)
primers (dont need primase, nuclease, ligase)
enzymes (polymerase)
nucleotides

94
Q

primers

A

single stranded - written 5’ to 3’

95
Q

reverse primers

A

at end of 3’ to 5’ strand - complements
written backwards from 5’ to 3’

96
Q

pcr steps

A
  1. heat to break double strand
  2. anneal (cool down) - primer w/ complement base pair
  3. polymerase in synthesis - extension
97
Q

amplifying gene

A

lyse cells isolate genomic DNA

98
Q

do primers become amplified in DNA?

A

yes, bc primers are DNA

99
Q

agarose gel electrophoresis

A

gel - with negative + positive end
DNA has negative charge
longer would be @ top

100
Q

what are plasmids?

A

can replicate independently of chromosomes - small circular double-stranded DNA

101
Q

what are plasmids used for

A

manipulation of genes - can be inserted in amplified gene

102
Q

restriction enzymes

A

ancient bacterial defense - protect against invading bacteriophages
cleave viral DNA - used in labs + need ligase to join

103
Q

how are PCR and plasmid cut?

A

restriction enzyme + ligate

104
Q

DNA cloning

A
  1. PCR sequence - contain proper restriction enzyme sites
  2. digest backbone w/ same enzyme
  3. ligate in test tube w/ vector
  4. transform into bacteria
105
Q

DNA sequencing

A

determines order of nucelotides

106
Q

sanger sequencing

A

used for smaller pieces of DNA
- added like in PCR (fluorescently labeled)
- fragments are separated by size (capillary gel)

bio 201 (1 decks)

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